Mass Effect 3: Electronic Data Interchange
by Pandamoniumous
Summary: This is my version of how Mass Effect 3 should have ended. What if the Protheans mistook the Catalyst for being just the Citadel? What if that itself was just another fabrication of hope?
1. Chapter 1

**Mass Effect 3: Electronic Data Interchange**

Disclaimer: I do not own any part of Mass Effect or its intellectual properties.

This is my version of how Mass Effect 3 should have ended. What if the Protheans mistook the Catalyst for being just the Citadel? What if that itself was just another fabrication of hope?

Takes place after leaving the Forward Operating Base. This Shepard is a male Infiltrator who romanced Liara. Three chapter series.

* * *

**Knocking on Heaven's Door**

A young Alliance marine removed his hand from his temples. His hand was shaking violently. He flex it several times before returning it to the fore grip of his gun. It seemed his whole body was shaking now. Insides churning, he wanted to puke all over the floor of the transport. He looked up to see a turian give him a squeeze on his shoulder. The first contact war seemed like a life time ago, in fact all the petty conflicts and wars were now just footnotes in the history books of the galaxy.

The doors of the transport opened up to fields of chaos. Flashes of blue biotics and orange tech abilities flew through the night sky. A precision shot of a geth sniper crumpled a Ravager before it could line up its sights on a group of Alliance marines taking cover behind a wall. A krogan battle master charged through Husk ranks, throwing his weight around, sending their human like bodies through the air. Alliance marines pepper a Banshee with gunfire, giving it pause for turian snipers to line up their shots. A group of salarian STGs dove out of the way of a charging Brute. It pounded its chest tauntingly, not noticing the set of explosives at its feet.

Commander Shepard could feel the shockwave from the explosion reverberate through the hull of the transport. He looked over his squad, all of them focused. The time for checking equipment has long since passed, by now you were either ready or you weren't. The resonating drone of a Reaper's beam told them they were getting close.

"We're getting out here," yelled Shepard to the driver.

He obeyed, opened the doors swung open. Shepard was the first to clear out of the transport and take up cover behind a shattered wall. He peeked over it to find a street disturbingly empty. Straight ahead was the Reaper focusing its attention on the main squad of Hammer forces. Shepard quickly and silently moved from cover to cover, occasionally scouting the buildings with scope of his rifle. After running out of cover they could use on the street, he motioned a group to move forward into an abandoned building. James lead the charge forward followed closely by EDI. Once they were inside Shepard poked his head out and scanned the area again. There was still no movement.

"We're clear Loco," James radioed in.

Shepard motioned for the second group to continue. Ashley sprinted towards the same building followed by Tali who had her omni-tool open, scanning for enemies. Garrus had his gun out quickly scoping out the top floors of an adjacent building as he continued along.

"We're in Commander," said Ashley over the comm.

"Continue ahead and keep in radio contact," said Shepard. "We are going to push ahead on ground level."

"Stay sharp out there Shepard," said Garrus who looked at the Commander briefly before following the rest of the squad into the building.

"We'll use the walls as cover," said Shepard to the remaining members. "Keep both eyes open for any movement."

"I'll keep four eyes open," retorted Javik.

Shepard was the first to break cover and slowly move his way forward, exposed on the street. At first he thought it was the echoes of the distant fighting, but he was sure of it now. The scream of a Banshee echoed down the street.

"We've got Banshees!" yelled James over the com followed by an eruption of gunfire.

"What's your location," asked Shepard back up against the building wall. "We'll come to you."

"We've got the situation under control," barked Garrus.

"Shepard," said EDI. "There are Reaper forces headed your way."

"Commander," yelled Javik shooting at a group of Cannibals coming up from the sewers.

He could hear another Banshee yell, this time much closer. He took aim with his rifle at the tall slender form of a Banshee slowly hovering down from a building roof top. Before he could take the shot, the building behind him erupted in an explosion of concrete, sending him flying to the street. The Brute hefted itself back up to its legs and pounded its chest triumphantly. Shepard barely had time to breath. But he quickly took aim at the Brute shooting off the armored plate revealing a ball of intestines. Enraged the Brute swung its massive claw nearly decapitating him in the process. Shepard charged up an incendiary blast with his omni-tool and stuck his arm in the staggering Brute. Shepard unleashed its full blast, causing the Brute become engulfed in flames. It staggered backwards trying to stamp out the flames with its arms before letting out a dying groan. Shepard picked himself up and searched the street seeing an incoming of Reaper forces. The Banshee had finally landed upon the street and turned its attention to Shepard. Liara threw out a biotic blast which the Banshee had knocked aside with a swing of its arm sending the bolt into a horde of its own troops. Javik poked his large head up from the pile of rubble before receiving a barrage of fire from a group of Marauders that had now entered the fray. Shepard backed away shooting at the Banshee as he did. He barely had enough time to roll out of the way of biotic blast, Shepard quickly activated his cloaking ability and took aim at the Banshee's head as it pondered the sudden disappearance of her target. Javik fired off the last rounds of his clip dissipating the protective barrier surrounding it. Shepard's shot hit the Banshee right between the eyes flicking its head back. It let out a final scream before crumpling to the ground.

Now exposed and uncloaked in the middle of the street, Shepard was receiving a barrage of gunfire from the Marauders and Cannibals. Quickly running out of options Javik hurled a grenade at the Commander's feet. The bioticly enhanced grenade detonated sending him flying back farther than he should have. He hit the wall of the building hard, if it weren't already loosened by the Brute, he would surely have died.

"What the hell did you do?" asked Liara angrily at the Prothean teammate.

"I just saved your Commander's life," said Javik reloading another thermal clip into his rifle. He raised his gun over the cover and fired it blindly at the Reaper forces. Many of the Marauders quickly dove out of the way, seeking cover while the Cannibals received the full brunt of the attack. Liara opened a biotic rift near the remaining forces, giving them an opening to get to Shepard.

"Are you hurt?" asked Liara checking on the Commander, giving him a quick scan of her omnitool.

"Nothing serious," said Shepard getting to his feet with some help.

"By the goddess," said Liara letting out a sigh of relief. But she turned her aggression towards Javik who was continuing to cover the entry. "What were you thinking? You could have killed him."

"But I didn't," said Javik over his shoulder. "I have seen the Commander in combat. Any lesser primitive would have died. If he did, it would have been an act of mercy."

Liara's body began to glow blue from charging up her biotics.

"That's enough," said Shepard stepping in. "Save it for the Reapers."

"Holy hell, Loco" said James running towards them from the street. "When that blast went off, we all thought you were dead."

"We have to keep pushing forward to clear a path for the tanks," said Shepard. "Where's everyone else?"

"Right here Shepard," said Tali and the other joining them. "We were just mopping up the last of them."

"Shepard come in," said Anderson over the comm. "What's your status."

"We just finished clearing a path for the tanks to move forward," said the Commander.

"Good," said Anderson. "We are getting flanked by Reaper forces."

"What's your location? We'll come to you," said Shepard.

"Its nothing that we can't handle. I need you to protect those tanks."

"Yessir."

They continued to walk down the street following the slow march of the tanks as they drove down the battered streets of London. The diversion seemed to be working as most of the Reaper forces seemed to be focusing on battalions of allied forces pushing towards the Reaper. Shepard motioned for the tanks to halt their progress near the edge of the crater.

"Shepard," said Garrus. "We need to get that Reaper's eye exposed long enough for the missiles or all we're going to do is scratch its paint job."

"EDI is this laser still hooked up to the Normandy's weapon system?" asked Shepard removing it from his back.

"They are, however, in our current location we do not have a direct line of sight," replied EDI.

"You're not seriously thinking about doing what you did on Ranoch again," objected Tali. "Its a miracle you came out of that alive."

"I agree its suicide Commander," said Ashley.

"Let me do this," said Garrus stepping forward. "You know I have the better shot."

"I should do it," said Javik bumping past Garrus. "I have earned the right. And I have the best shot out of the both of you."

"If you are insistent upon getting yourself blown up," said James. "We're coming with you, Loco."

"No," said Shepard silencing all of the bickering. "I need you all here to protect those tanks until they can fire their payload."

"Shepard, I am coming with you," said EDI stepping forward.

"I need you to stay back and help defend the tanks," he said. "This isn't up for discussion."

"I was not making a request," said EDI firmly. "I can use the body's optics to further refine and make any alterations to the missile's flight pattern depending on the situation."

Shepard opened his mouth as if to object, but saw how firmly she wanted to do this. "Alright," he said walking past his team. "Everyone else stay with those tanks until I get back."

"Shepard," said Garrus grabbing his arm. "You don't have to do this."

"Let's see if all of those calibrations pay off," said Shepard.

"Give them hell, Loco," said James giving him a salute.

"Pay them back for what they did to Earth," said Ashley

"It should be me doing this," said Javik. "But… This is not my cycle. It is yours."

"Keelah se'lai," said Tali. "We'll be waiting for you to get back."

"Shepard…" said Liara tears barely kept in check. "I-."

"I know," said Shepard. His hand gently caressing her face.

"I'll be waiting for you right here," said Liara as he brushed a tear from her eye. His fingertips ran down her cheek until his fingertips gently brushed off her chin. She reached out with her hand as if trying to grab hold of his hand one last time, but missed. She could only look on as the two figures made their lonely trek down the side of the crater towards the beam with the Reaper looming over it.


	2. Chapter 2

**Mass Effect 3: Electronic Data Interchange**

Disclaimer: I do not own any part of Mass Effect or its intellectual properties.

* * *

**Into the Gates of Hell**

Shepard took cover behind a crashed Alliance Mantis gunship. Shepard poked his head into the shattered cockpit. To which EDI replied that there are no survivors. Shepard carefully inched his way along the hull of the ship until he could get a full view of the Reaper. The thundering shot of the Reaper's beam was just as deafening as he had remembered it.

"Commander we are reentering the atmosphere," said Joker over the comms. "ETA two minutes."

"Shepard," commented EDI. "I suggest aiming the laser at the ocular as it is firing its beam."

"Just like before," said Shepard removing the massive laser from his back and stepping out of cover. He shoulders the weapon and takes aim at the Reaper painting the target for the Normandy.

"Shepard," yelled Anderson over the comms. "What the hell are you doing?"

"Worry about keeping yourself alive," Shepard yelled back.

"I've got a confirmed lock," yelled Joker.

The Reaper opened its protective covering once more and charged the oculus for an attack. The Normandy's cannons roared to life sending several shots screaming overhead. The shots slammed into the Reaper nearly knocking it off balance. It staggered backwards for a moment before readjusting its footing. It looked up at the sky for a moment before returning its gaze back down to the ground, acquiring its new target. It fired its charged up beam at Shepard who barely managed to dive out of the way. He cringed in pain as his whole body began to smoke from the beam. EDI broke cover and began to run towards the Commander but quickly retreated back when Reaper forces began to drop in from a Harvester flying overhead.

"Coming around for another pass," said Joker to the Commander.

Shepard picked up the laser and shouldered it once more, taking aim at the Reaper. "Come on you son of bitch," he said gritting his teeth, trying to shake off the pain.

EDI popped up from cover to fire several shots before ducking down and employing her Decoy a few meters away. The Decoy mimicking her every move popped up at the same time confusing the Marauders and Cannibals, giving her time to take out as many of them as she could before returning to cover. Skirting along the remains of the gunship she rolled out of cover and next to the Commander. She continued to lay down a barrage of gunfire from her SMG until shutdown due to overheating.

"Shepard," said EDI reloading a fresh thermal clip into the gun. "I suggest moving to an area that has more cover."

"If that Reaper fires its beam at us again," he said. "Cover is going to be pointless. Just hold them off for a bit longer."

"Yes Commander," said EDI recharging his shields before scurrying forward to hide behind cover just large enough for her to take cover.

Finally taking notice of the difference, the Reaper forces fired upon EDI and the Commander, ignoring the decoy completely. She fired several shots from cover before popping up and sending a blast of kinetic energy at a group advancing upon their location. They froze in place, feeling the surge of electrical energy course through their bodies, making them easy targets for EDI to pick off one by one. The more she took out, the more Harvesters kept deploying. Waiting until the last possible second, Shepard rolled out of the way of the beam. Several more shots from the Normandy hit the Reaper's oculus. One of the protective plates was knocked loose, leaving it open for attack.

Shepard lying on the ground gritting his teeth in pain yelled to his companion. "EDI, sync all of the remaining tanks."

His body was in agony. Every inch of it was screaming at him to stay down. Even though it was only a glancing blow, his body was singed from the beam. Shepard picked himself up and shouldered the laser once more.

Sensing its impeding doom, the Reaper quickly charged up its beam. EDI ran over to the Commander ignoring the hail of gunfire from the Reaper forces. She quickly reached out and recharged his shields just as her own became depleted.

"Fire!" yelled Shepard to EDI, sending out the command code to all the tanks, launching a barrage of missiles at the Reaper. With its remaining energy it fired off one last beam before missile after missile hit its mark, blowing it apart.

Without a second thought, EDI pushed the Commander out of the way.

When the Reaper fell, it felt like a 20 ton bomb had gone off. The cloud of dust it produced covered the entire battlefield in a thick cloud of dust. Everyone was slow to get up, with everything in a haze, there was a short calm before shots rang out and the fighting started up again. Fighting with new zeal the allied soldiers picked up their weapons and fought hard, knowing that they had just killed a Reaper.

"Ssssshhhh…. E-. Pard," said a broken electronic voice in the dust. "Sssshhh… arddd…"

It was hard to breath, his lungs were on fire. With a mouth full of dust, he tried to spit but found no saliva left. Looking around, he saw sparks of light and somehow knew its was her. EDI, or what was left of her, was lying on the dirt beside him. Her omni-tool optical visor flickered on and off, her head barely connected to her neck by a few loose wires, the lower half of her body, completely gone.

"Don't…" she said, her speech cutting in and out. "So… Concerned. Th… Isssss… is just… physssss… cal… body."

"Shepard?" yelled Anderson over the comms. "Are you still alive? You need to get to that beacon. Shepard, do you copy?"

"I copy," said the Commander getting to his feet before falling over again.

"Shepard? You need to get to that beacon," said Anderson again. "We are pinned down by Reaper forces."

"I copy Anderson," he said again firmly planting his feet on the ground before standing upright. "Anderson?"

"Shepard, come in," said Anderson not hearing anything over the comms.

"Hammer, there are Reapers entering the atmosphere," said Hackett over the comm. "We are trying to delay them as much as possible. You need to get to that beacon and open the arms of the Citadel."

The blare of a Reaper sent a chill up Shepard's spine. His heart sank as he could see a massive silhouette descending from the sky. When it landing the entire ground shook like an earthquake, nearly knocking him over. Even though he couldn't see it clearly, Shepard could tell it was Harbinger. It quickly charged up its beam and fired it at the direction of tanks. Explosions echoed through the battlefield.

"We are under heavy Reaper attack!" yelled Garrus over the comms. "All of the tanks have been destroyed! Need assistance!"

"EDI," said Shepard heaving her torso onto his back. "Can you connect to the Normandy?"

"Yessss…" she said in his ear.

"Tell Joker to do a pick up on their location," said Shepard through heavy breaths.

She remained silent for a moment. "He… coming… ppppp…. ick us up…" she said relaying the message.

"No," said Shepard making his trek toward the beacon. "Tell him do not pick us up. Tell him that's an order."

"Done…" she managed to say.

Shots echoed through the battlefield like thunder as some of the dreadnoughts in orbit began to lay down covering fire for the Normandy. Harbinger steadied itself, bracing for the impacts of the shells which exploded all around it. The shots that did hit barely did more than make a few dents in the armor, but all it could do was glare up at the sky menacingly, not wanting to make the mistake of opening its oculus.

Flashes of red light burst in existence all around him, the Harvesters had no idea where exactly to deploy its payload of troops. Banshees shrieked in the distance, followed by explosions of blue biotic energy. Brutes could be heard pounding the ground in frustration, knocking over or breaking through anything that could have potentially be used for cover. Through the thick fog of war, Shepard did the only thing he could, follow the faint blue glow of the beacon.

At last the dust began to clear, hefting EDI back into place on his shoulders, Shepard charged forward. The thunder from the dreadnoughts had ceased, the hairs on his neck stood on end. He could feel Harbinger charging up its beam. Shepard broke out into a sprint, ignoring the spikes of pain from every muscle in his body. His body began to smolder, the Reaper's beam was only a few meters behind him, closing in fast. With one final step he lunged forward, jumping into the soothing blue light of the beacon.

"Holy shit," breathed Hackett drawing his attention momentarily away from the battle around Earth's orbit. "He's in."

"This is Hammer," yelled Anderson over the comm. "The beacon has been destroyed. I repeat, the beacon has been destroyed."

"Hammer," said Hackett. "Fall back, there isn't any more that you can do down there. We believe Shepard has made it through."

"Affirmative," said Anderson out of breath. "I don't know how much longer we can hold out…"

"Stay alive, that's an order," said Hackett over the comm, shoulders slouching forward and head hung low. "Do you think he can get it done?"

Crewmen on the bridge continued to work at their stations, but glanced over to the Admiral periodically, dissecting his body language. Even though he didn't look at them, Hackett could feel the enthusiasm of his crew slipping. Their movements had now become sluggish and their tone of voice had turned to discouragement, they felt defeated.

"If anyone can get those arms open," said Anderson between shots. "Shepard can. He's all the hope we have left."

After hearing Anderson's words, he regained his composure and cast all doubt from himself. He threw out his chest and straightened out his shoulders. He turned to his crew with a renewed sense of pride. "Order all remaining ships to protect the Crucible at all costs. We need to give Shepard more time."

Without the Admiral knowing, someone on the bridge had set the comms to be addressed to the entire fleet and as well as those on the ground and to all who could hear it.

"As Admiral you all looked to me to be your pillar of confidence, and I have faltered and lost hope. Those things out there are threatening to take away our families and friends, our hopes and dreams. We have always thought that we have a right to exist in this galaxy. But that right isn't something that is given, it is earned. Today we will earn that right. We have amassed the largest fleet in recored history, both human and alien alike. He do not fly under the banner of the Alliance, or the Citadel, or any other fleet's banner. We have cast aside old grudges and hatreds and fly under one notion. Hope. Hope that this nightmare will end and see the dawn. Hope that we will face this fear and bring it to and end. Hope may falterer, but it is never lost so long as one person remains and stands up against these monsters. Stand with me and send them back to hell where they belong."

Hackett looked over his men one last time before returning to looking out the window. Glancing down at his terminal he noticed that the comms had been set to an open channel before turning off.

"Sir, we have Salarian ships incoming," said a crewman handing him a data pad. "It looks like their entire navy."

"Have them cover damaged ships so they can make repairs," said Hackett to the crewman who saluted and quickly ran off to spread the order. "Let's finish this Shepard."

His head was pounding and lying there felt like as good a place as any to give up. His chest was heavy and it was getting harder to breath.

"Commander?" said EDI in his ear piece. "Shepard?"

He opened his eyes to find himself starting face to face with EDI's. Her head had finally become detached from her body, which was still on his back. He shoved the decapitated torso from his back which alleviated some of his breathing problems, but did nothing for the rest of his body.

"Are you okay?" he asked EDI.

"Aside from being decapitated," she told him through the comms again. "Yes."

"Is you're head still functional?" he asked picking up her head.

"In order to preserve as much power as possible I have shut down all unnecessary functions," she told him. "I am able to hear and see, but my vocal capabilities have been severely damaged."

"Where are we?" he asked looking around at the mounds of bodies pilled all along walls. The Keepers continuing to preform their duties not noticing or not caring about the bodies piled around them.

"It appears that we are in an undocumented location on the Citadel," answered EDI. "This location would most likely be at the Citadel Tower."

"Can't go that way," said Shepard looking at a massive pile of bodies blocking one part of the hallway.

"I detect that a control counsel is near by," she told him.

The further down the hallway they went, the bodies and corpses began to thin out. Several times the Commander nearly toppled over, from either the pounding in his head or from the smell of rotting decrepit flesh. But he did fall over one time, finding himself staring at a human body, lifeless eyes staring up at him, look of horror frozen on her face. She couldn't have been more than ten years old.

Finding a renewed rage, Shepard got to his feet and continued down the hallway, taking long thundering strides. It wasn't long before the hallway of bodies opened up to a huge caverns of moving walls. Sparks of electricity jumped from wall to wall. There must have been thousands of walls moving up and down. They moved like a tidal wave, only one set of walls would rise above the others and would slowly move down the chain till it reached the bridge and pass the electricity from one side to the other. He stood there for a moment, the time between electrical exchanges was exactly fifteen seconds. He'd have to make it across in less than that or be fried. He paced the count from the first electrical exchange that crossed the bridge, waiting for the next one.

If he could still run, this wouldn't have been a problem, but he couldn't neither run nor jog. All he could do was hobble along as quickly as he could. He could hear the shifting of the walls getting louder and louder. With one last step he propelled himself forward, landing on the other side of bridge and on the hard metal steps leading up. He could feel the hairs on his neck stand on end as the electricity passed over the bridge.

He crawled up the stairs which opened up to a large room with an almost panoramic view of the closed citadel. He peered over the side and looked down to see a bottomless abyss bellow.

"I've been wondering when you'd finally get here," said the Illusive Man who had been leaning against the lone command counsel in room. He blew out a lung full of smoke and dropped the butt of his cigarette on the ground, snuffing it out with his shoe. Blue scars ran down his face and neck, almost reminiscent of the transformation stages of a human into a husk. His blue eyes seemed brighter now, what little humanity they had left in them was now gone.

"Illusive Man," said Shepard trying to get to his feet. "Let me guess, you're here to try and stop me."

"I've been talking with the Reapers," said the Illusive Man walking towards them. "They only want to preserve us, not destroy us."

"He is indoctrinated," said EDI.

"You call that," said Shepard motioning back towards the hallway with the mounds of dead bodies. "Preservation?"

"Think Shepard," said the Illusive Man pointing at his temple. "Long after our bodies are gone, our ideas and our technology will still be preserved. The human race will be preserved forever. This is what humanity is striving to become. It is our next evolutionary state to become what the Reapers are. It is the evolutionary state for all sentient organic life."

"Are you listening to yourself?" asked Shepard. "You've become one of them."

"That's where you're wrong," said the Illusive Man. "I can control them."

"If you can control them," said Shepard. "Why haven't you done so already?"

"I have been studying them," he said pacing around the center of the room. "After learning what the Catalyst was, I came here for myself. And do you know what I discovered Shepard? There is no Catalyst. Its all just a lie made up by the Reapers to give us a false sense of hope. This is all just one big hoax and we've all been played for fools." He stopped pacing and straightened his jacket. "Except for me. I have found a way to end all of this. And I need what's in your hands. I need EDI."

"Shepard, I have been analyzing the data in the Citadel's data base," said EDI into his ear. "The origin of Catalyst appears to permeate from the Citadel itself. There is some truth to the Illusive Man's words."

"Why do you need her?" asked Shepard.

"I need it's code so I can enhance my abilities to affect all Reapers, not just those in close proximity," said the Illusive Man holding out his hand. "Now hand over the head, if you please."

"You don't get it," said Shepard. "You can never control them, no matter how much you think you're in control, they already own you."

"That's not true! I'm doing this for humanity's sake! I've always done everything for the good of humanity," said the Illusive Man drawing a gun from his jacket. "Including this."

Shepard could have sworn he saw the Illusive Man shed a tear the blast ripped apart half of his face. His body went limp and collapsed into a heap on the floor. It wasn't long until the Illusive Man's lifeless body began to move. A skeleton of Reaper tech pulled itself free of the Illusive Man's body. It reminded Shepard of a miniature version of the Proto Human-Reaper they had destroyed a lifetime ago. It screeched up at him before clawing its way across the floor to them. Before the thought had full formed in his head, he dove forward reaching for the Illusive Man's gun. His fingers wrapped around the handle of the gun. His heart racing, he pulled the trigger. Several shots rang out, a few shots either ricocheted off the metal bones or passed right through the gaps. But one shot did manage to seek its way and hit it squarely in the chest, where its "heart" was. It reached out trying to grab a hold of Shepard but collapsed on the floor, red eyes dimmed into black sockets.

"There are no Reaper forces detected," said EDI over the comm. "Shepard, you need to open the arms so the Crucible can dock."

Shepard for the was seemed the thousandth time, had to get back up to his feet. He nearly fell forward trying to pick up EDI's head, but regained his balance in time. He staggered forward as best he could and leaned up against the counsel. The controls flickered on and off. He tried activating several controls, but there was no response.

"Its been damaged," said Shepard placing EDI's head on the counsel. "There's no way I can get the arms open." With his legs giving way, he sank back down to the floor. "Even if I could. What if he was right? What if this was all just one big hoax? What if…"

"Rest now," said EDI into his ear before he blackout from the pain. Before he did, he could have sworn he saw her watching over him, her body fully intact.


End file.
